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Created with Raphaël 2.2.023Dec222119181716151312107430Nov27262523221298765329Oct252422211564128Sep2220191715131211876530Aug282622191531Jul1514Jun30May2928242322211816151430Apr191715113227Mar2622211312126Feb23201918151413128742129Jan26252417830Nov2721326Oct20191623Sep1910627Aug252423222126Jul252416151122Jun2017137626May119Apr1827Mar221827Feb26252321161123Dec865325Nov2422211613Oct119Sep87643131Aug2623187653229Jul282520130Jun282721201817161412987331May301918161326Apr23181225Mar131124Feb17162129Jan282614PuReMD-old: change from array of structs to struct of arrays for far nbr list (far_neighbor_data).PuReMD: find SAi threshold among sampled entriesPuReMD-old: minor log file formatting tweaks. Default to full shell for now.PuReMD: split Init_Forces into 3 functions: Init_Distance, Init_CM and Init_Bond, and add timings for those functionssPuReMD: clean-up geometry file I/O code. Remove a few compiler warnings.PuReMD-old: fix timing issues. Remove fine-grained timing of Init_Forces due to high overhead. Disable SAI preconditioner optimization of changing far nbr list and matrix formats based on preconditioner refactoring step (not working). Tweak to not product numeric overflow when setting up SAI preconditioner (pivot sampling).sPuReMD: screen out non-periodic self-interactions when constructing far nbr list.sPuReMD: default to vlist_buffer of 2.5 angstroms. Fixes to cutoffs used in far neighbor list generation.PuReMD: fix qeq init timingPuReMD: fix the broken preconditioner setupPuReMD: change timing functions with MPI_Wtime()PuReMD-old: tools update in run_sim_mpi.py for larger silica and water systems.PuReMD: include charge matrix fill in timing for performance comparisonPuReMD-old: revert debugging code.PuReMD-old: note barrier removal for later.PuReMD: SAFE_ZONE change for NTsPuReMD: remove unused code.Merge branch 'master' of https://gitlab.msu.edu/SParTA/PuReMD.sPuReMD: re-enable SMALL_BOX_SUPPORT. Fix issue with far nbrs list being incorrectly generated for small boxes (missing nbr ID). Fix issue with ACKS2 matrix being incorrect for small boxes due to multiple non-zeros being added for each perioidic image of an atom (accumulate instead). Add missing ACKS2-specific energy and forces term. Clean-up far nbr list estimation and generation code for small boxes. Do not add far list struct entries unless the atom is below the specified cutoff.PuReMD-old: fix typo (malloc -> smalloc).PuReMD-old: more clean-up of linear algebra code. Remove or conditionally enable debugging code (DEBUG preprocessor). Fix memory leak in SAI setup. Better memory allocation checks.PuReMD: fix charge matrix reallocation bugPuReMD: fix a minor bug regarding Init_ForcesPuReMD-old: remove non-source junk files. Clean-up to remove debugging code for neutral territory. Conditionally toggle SpMV implementation (Sparse_MatVec) debugging on if neutral territory is selected.PuReMD: enable NT for half matrixPuReMD: fix the communication bug for NTPuReMD-old: more control file format changes.PuReMD: fix allocation problem regarding NT buffersPuReMD: continue NT for Jacobi debuggingTools: fix short jobs script typo. Set default HBond cutoff to 7.5 angstroms in run_sim.py.PuReMD-old: backport control file format changes.PuReMD: fix errors regarding matrix formatPuReMD: minor change: remove output statements for debuggingPuReMD: add preprocessors for Neutral TerritoryFix compilation errors (MAX_NT_NBRS -> REAX_MAX_NT_NBRS).Merge branch 'full-far-nbrs-list-charge-matrix' into full-far-nbrs-list-charge-matrix-half-full-refactor.Merge branch 'full-far-nbrs-list-charge-matrix-half-full-refactor' into full-far-nbrs-list-charge-matrix-half-full-refactor2.Fix issue with bonds list ordering leading to different torsion and conjugation energies due to changing the far neighbors list to a full list.Merge commit 'cc6d9994' into full-far-nbrs-list-charge-matrix-half-full-refactor.Merge with branch full-far-nbrs-list-charge-matrix at commit 1134d3bf.